Base Info

An object of class Seurat 42748 features across 5536 samples within 2 assays Active assay: SCT (15481 features, 3000 variable features) 1 other assay present: RNA 3 dimensional reductions calculated: pca, umap, tsne

The Seurat object was generated with Seurat 3.1.4.

Table of Data

Tissue Data

Annotated Cell Types

Calculated Clusters

Interactive Plot

Downsampled to 5000 cells.

Environment

## R version 3.6.3 (2020-02-29)
## Platform: x86_64-apple-darwin18.7.0 (64-bit)
## Running under: macOS Mojave 10.14.6
## 
## Matrix products: default
## BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
## LAPACK: /usr/local/Cellar/openblas/0.3.9/lib/libopenblasp-r0.3.9.dylib
## 
## locale:
## [1] en_CA.UTF-8/en_CA.UTF-8/en_CA.UTF-8/C/en_CA.UTF-8/en_CA.UTF-8
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
##  [1] plotly_4.9.2.1    knitr_1.28        ggplot2_3.3.0     rmarkdown_2.1     future_1.17.0     sctransform_0.2.1 gsubfn_0.7       
##  [8] proto_1.0.0       DropSeq.util_2.0  Matrix_1.2-18     data.table_1.12.8 dplyr_0.8.5       Seurat_3.1.5      R.matlab_3.6.2   
## 
## loaded via a namespace (and not attached):
##   [1] Rtsne_0.15          colorspace_1.4-1    ellipsis_0.3.0      ggridges_0.5.2      rprojroot_1.3-2     fs_1.4.1           
##   [7] rstudioapi_0.11     farver_2.0.3        leiden_0.3.3        listenv_0.8.0       npsurv_0.4-0        remotes_2.1.1      
##  [13] ggrepel_0.8.2       fansi_0.4.1         codetools_0.2-16    splines_3.6.3       R.methodsS3_1.8.0   lsei_1.2-0         
##  [19] pkgload_1.0.2       jsonlite_1.6.1      ica_1.0-2           cluster_2.1.0       png_0.1-7           R.oo_1.23.0        
##  [25] uwot_0.1.8          compiler_3.6.3      httr_1.4.1          backports_1.1.6     assertthat_0.2.1    lazyeval_0.2.2     
##  [31] cli_2.0.2           htmltools_0.4.0     prettyunits_1.1.1   tools_3.6.3         rsvd_1.0.3          igraph_1.2.5       
##  [37] gtable_0.3.0        glue_1.4.0          RANN_2.6.1          reshape2_1.4.4      Rcpp_1.0.4.6        vctrs_0.2.4        
##  [43] gdata_2.18.0        ape_5.3             nlme_3.1-147        crosstalk_1.1.0.1   lmtest_0.9-37       xfun_0.13          
##  [49] stringr_1.4.0       globals_0.12.5      ps_1.3.2            testthat_2.3.2      lifecycle_0.2.0     irlba_2.3.3        
##  [55] gtools_3.8.2        devtools_2.3.0      MASS_7.3-51.5       zoo_1.8-7           scales_1.1.0        parallel_3.6.3     
##  [61] RColorBrewer_1.1-2  yaml_2.2.1          curl_4.3            memoise_1.1.0       reticulate_1.15     pbapply_1.4-2      
##  [67] gridExtra_2.3       stringi_1.4.6       desc_1.2.0          caTools_1.18.0      pkgbuild_1.0.6      rlang_0.4.5        
##  [73] pkgconfig_2.0.3     bitops_1.0-6        evaluate_0.14       lattice_0.20-41     ROCR_1.0-7          purrr_0.3.4        
##  [79] labeling_0.3        patchwork_1.0.0     htmlwidgets_1.5.1   cowplot_1.0.0       tidyselect_1.0.0    processx_3.4.2     
##  [85] RcppAnnoy_0.0.16    plyr_1.8.6          magrittr_1.5        R6_2.4.1            gplots_3.0.3        pillar_1.4.3       
##  [91] withr_2.2.0         fitdistrplus_1.0-14 survival_3.1-12     tibble_3.0.1        future.apply_1.5.0  tsne_0.1-3         
##  [97] crayon_1.3.4        KernSmooth_2.23-16  usethis_1.6.0       grid_3.6.3          callr_3.4.3         digest_0.6.25      
## [103] tidyr_1.0.2         R.utils_2.9.2       munsell_0.5.0       viridisLite_0.3.0   sessioninfo_1.1.1